|
| Status |
Public on Jun 09, 2012 |
| Title |
Acute hepatitis C patient 4 |
| Sample type |
RNA |
| |
|
| Source name |
liver biopsy, acute hepatitis C, patient 4
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver biopsy
disease state: acute hepatitis
|
| Growth protocol |
All patients were recruited in the Hepatology Outpatient Clinic of the University Hospital Basel, Switzerland. From October 2007 to December 2010, 6 patients with AHC (between 0-6 months after the HCV transmission) gave written informed consent to participate in this study and donated a liver biopsy specimen for research purposes. The study was approved by the Ethics Committee of Basel. Liver biopsies from 16 patients with CHC and 4 normal liver tissue samples were used for comparative analysis. These samples have been obtained during a previous study that has been published 7. The data reported in that paper have been deposited in the Gene Expression Omnibus database, www.ncbi.nlm.nih.gov/geo (accession no. GSE11190).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the liver samples using Qiazol reagent and miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction
|
| Label |
biotin
|
| Label protocol |
1 ug of total RNA was reverse transcribed, amplified, labelled and fragmented with GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The Hybridization, Wash and Stain Kit (Affymetrix) was used to hybridize all samples for 17 hours at 45°C in Affymetrix hybridization oven 645. The arrays were washed and stained on Fluidics station 450 using wash protocol FS450_0004 (Affymetrix).
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.
|
| Data processing |
Microarray data were preprocessed using standard RMA algorithm as implemented in the AFFY package of Bioconductor libraries of R statistical environment. Batch effects observed between the human liver samples processed and hybridized at different times were corrected using the ComBat algorithm (Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007;8:118-27.)
|
| |
|
| Submission date |
Jun 08, 2012 |
| Last update date |
Jun 09, 2012 |
| Contact name |
Zuzanna Makowska |
| Organization name |
University of Basel
|
| Department |
Biomedicine
|
| Lab |
Hepatology
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE38597 |
Gene expression profiling of 6 acute hepatitis C patients |
| GSE38598 |
Hepatocytes treated with IFN-alpha or IFN-gamma and acute hepatitis C |
|
